Mohammad Salma, PhD

Senior Bioinformatician & Data Scientist

Transforming complex genomic data into actionable insights through advanced bioinformatics, machine learning, and innovative pipeline development

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About Me

Senior Bioinformatician and Data Scientist with extensive expertise in analyzing next-generation sequencing (NGS) data and developing cutting-edge bioinformatics pipelines.

My journey combines a strong foundation in genomics with advanced skills in artificial intelligence and machine learning. I specialize in translating complex biological data into meaningful insights for oncology and rare disease research.

Throughout my career, I have supervised bioinformatics engineers and doctoral students, refining my expertise in project management and team leadership. I am passionate about innovation, particularly in applying AI/ML methods to genomics to improve diagnostics and research in fields such as oncology and rare diseases.

PhD in Biotechnology

University of Montpellier

6+ Years Experience

Bioinformatics & Data Science

19+ Publications

223 Citations, h-index: 7

Professional Experience

June 2025 - Present

Project Manager

Institut Imagine | Bioinformatics & Data Science

Montpellier, France

  • Leading bioinformatics and data science projects for genetic disease research
  • Coordinating multidisciplinary teams and project deliverables
  • Implementing advanced genomic analysis workflows
December 2023 - May 2025

Senior Bioinformatics & Data Scientist

IRCM - Institut de Recherche en Cancérologie de Montpellier

Montpellier, France

  • Supervised bioinformatics engineers and provided technical leadership
  • Implemented advanced AI/ML algorithms for cancer genomics analysis
  • Mentored doctoral student in bioinformatics (since October 2022)
  • Developed robust pipelines for ATAC-Seq, RNA-Seq, and multi-omics integration
Single Cell Sequencing ATAC-Seq Machine Learning
November 2021 - September 2023

Bioinformatics & Data Scientist

Institut Imagine | Laboratory of Excellence GR-Ex | Université Paris Cité

Paris, France

  • Developed custom tools and pipelines for complex genomic data analysis
  • Applied machine learning with TensorFlow and scikit-learn for biomarker identification
  • Supervised doctoral student providing pedagogical and scientific mentorship
Exome-Seq RNA-Seq TensorFlow
September 2018 - October 2021

Bioinformatics & Data Scientist

IGMM - Institut de Génétique Moléculaire de Montpellier (CNRS)

Montpellier, France

  • Implemented NGS workflows for DNA, RNA, and epigenome analysis
  • Conducted variant detection, functional annotation, and automated reporting
  • Collaborated with multidisciplinary teams of biologists and data scientists
ChIP-Seq ATAC-Seq Variant Calling

Skills & Expertise

Programming

Python R Bash PHP JavaScript

NGS Analysis

RNA-Seq scRNA-Seq ATAC-Seq ChIP-Seq Exome-Seq Cut&Run CaptureC-Seq Spatial Transcriptomics

AI & Machine Learning

TensorFlow scikit-learn Random Forest LASSO Deep Learning

Workflows & Tools

Snakemake Nextflow nf-core Docker Singularity

Data Management

MySQL MongoDB HPC

Development

Flask Streamlit RShiny GitHub GitLab

Selected Publications

2025

The methyl-CpG-binding protein 2 inhibits cGAS-associated signaling

Hanane Chamma, Soumyabrata Guha, Roger Junior Eloiflin, Adeline Augereau, Pierre Le Hars, Moritz Schüssler, Yasmine Messaoud-Nacer, Mohammad Salma, Joe McKellar, Joanna Re, Morgane Chemarin, Arnaud Carrier, Michael A. Disyak, Clara Taffoni, Robin Charpentier, Zoé Husson, Emmanuel Valjent, Charlotte Andrieu-Soler, Eric Soler, Maria H. Christensen, Søren R. Paludan, Florian I. Schmidt, Daniela Tropea, Karim Majzoub, Isabelle K. Vila and Nadine Laguette

Nature Communications (2025)

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2025

VEXAS syndrome anemia is a mosaic erythroblastopenia

François Rodrigues, Giulia Hardouin, Sara El Hoss, Aya Ghoul, Emilie-Fleur Gautier, Michaël Dussiot, Maria A Lizarralde-Iragorri, Annalisa Santini, Sandy Peltier, Pascal Amireault, Vanessa Soldan, Annarita Miccio, Mounia Debili, Vincent Jachiet, Thiago Trovati Maciel, Julien Rossignol, Eric Allemand, Arsène Mekinian, Sophie Georgin-Lavialle, Mohammad Salma, Eric Soler, Pierre-Emmanuel Gleizes, Marie-Françoise O'Donohue, Olivier Kosmider, Manuel S Rodriguez and Olivier Hermine

Blood (2025)

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2025

MMS22L is a novel key actor of normal and pathological erythropoiesis

Elia Colin, Ivan Ferrer‐Vicens, Dror Brook, Mohammad Salma, Charlotte Andrieu‐Soler, Elisa Bayard, Alicia Fernandes, Chantal Brouzes, Carine Lefèvre, Romain Duval, Michaël Dussiot, Thiago Trovati, Geneviève Courtois, Slim Azouzi, Mohammed Zarhrate, Anne Lambilliotte, Sophie Park, Benjamin Carpentier, Martin Colard, Sandra Manceau, Despina Moshous, Patrick Mayeux, Emilie‐Fleur Gautier, Annarita Miccio, Jean Soulier, William Vainchenker, Liran Shlush, Lydie Da Costa, Jan Frayne, Eric Soler, Olivier Hermine and Lucile Couronné

HemaSphere (2025)

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2025

IFN-I-Mediated Transcriptional Reprogramming Drives Myeloid-skewed Hematopoiesis in Sickle Cell Anemia

Marion Serra, Marine Aglave, Mohammad Salma, Steven Akkaya, Patricia Hermand, Carine Lefevre, Romain Duval, Jade Merrer, Fallou Leye, Joelle Magne, Isabelle Plo, Lionel Blanc, Eric Soler, Slim Azouzi and Berengere Koehl

(2025)

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2025

In vivo deletion of a GWAS-identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in β-thalassemia

Virginie Deleuze, Tharshana Stephen, Mohammad Salma, Cédric Orfeo, Ruud Jorna, Alex Maas, Vilma Barroca, Marie-Laure Arcangeli, Charles-Henri Lecellier, Charlotte Andrieu-Soler, Frank Grosveld, Eric Soler

Scientific Reports (2025)

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2023

Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Virginie Deleuze, Leonor Garcia, Betty Rouaisnel, Mohammad Salma, Alexia Kinoo, Charlotte Andrieu-Soler and Eric Soler

IScience (2023)

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2023
Featured Tool

Var|Decrypt: a novel and user-friendly tool to explore and prioritize variants in whole-exome sequencing data

Mohammad Salma, Elina Alaterre, Jérôme Moreaux and Eric Soler

Epigenetics & Chromatin (2023)

Developed a web-based tool that significantly streamlines WES data analysis, offering extensive gene and variant filtering, clustering, and enrichment tools without requiring complex bioinformatics skills.

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2023

High-throughput methods for the analysis of transcription factors and chromatin modifications

Mohammad Salma, Charlotte Andrieu-Soler, Virginie Deleuze and Eric Soler

Blood Cells, Molecules, and Diseases (2023)

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2022

ONTdeCIPHER: an amplicon-based nanopore sequencing pipeline for tracking pathogen variants

Emira Cherif, Fatou Seck Thiam, Mohammad Salma, Georgina Rivera-Ingraham, Fabienne Justy, Theo Deremarque, Damien Breugnot, Jean-Claude Doudou, Rodolphe Elie Gozlan and Marine Combe

Bioinformatics (2022)

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2021

PPARγ agonists promote the resolution of myelofibrosis in preclinical models

Juliette Lambert, Joseph Saliba, Carolina Calderon, Karine Sii-Felice, Mohammad Salma, Valérie Edmond, Jean-Claude Alvarez, Marc Delord, Caroline Marty, Isabelle Plo, Jean-Jacques Kiladjian, Eric Soler, William Vainchenker, Jean-Luc Villeval, Philippe Rousselot and Stéphane Prost

Journal of Clinical Investigation (2021)

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2021
Most Cited - 86 Citations

p53 activation during ribosome biogenesis regulates normal erythroid differentiation

Salomé Le Goff, Ismael Boussaid, Celia Floquet, Anna Raimbault, Isabelle Hatin, Charlotte Andrieu-Soler, Mohammad Salma, Marjorie Leduc, Emilie-Fleur Gautier, Boris Guyot, Diane d’Allard, Nathalie Montel-Lehry, Sarah Ducamp, Amandine Houvert, François Guillonneau, Stéphane Giraudier, Elisabeth Cramer-Bordé, François Morlé, Jean-Jacques Diaz, Olivier Hermine, Naomi Taylor, Sandrina Kinet, Frédérique Verdier, Rose-Ann Padua, Narla Mohandas, Pierre-Emmanuel Gleizes, Eric Soler, Patrick Mayeux and Michaela Fontenay

Blood (2021)

Demonstrates how p53 activation during ribosome biogenesis plays a crucial role in regulating normal erythroid differentiation processes.

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2014

Comparison of droplet-vitrification and D-cryoplate for cryopreservation of date palm polyembryonic masses

Mohammad Salma, Lotfi Fki, Isabelle Engelmann-Sylvestre, Takao Niino and Florent Engelmann

Scientia Horticulturae (2014) - 39 Citations

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2014

Effect of the successive steps of a cryopreservation protocol on the structural integrity of Rubia akane Nakai hairy roots

Mohammad Salma, Isabelle Engelmann-Sylvestre, Myriam Collin, Jacques Escoute, Marc Lartaud, Jung-Yoon Yi, Haeng-Hoon Kim, Jean-Luc Verdeil and Florent Engelmann

Protoplasma (2014) - 21 Citations

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2017

Cryopreservation of Date Palm Pro-Embryonic Masses Using the D Cryo-plate Technique

Mohammad Salma and Florent Engelmann

Methods in Molecular Biology (2017)

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View All Publications on Google Scholar

19+

Publications

223

Citations

7

h-index

6

i10-index

Notable Projects

Var|Decrypt

A web-based tool for exploring and prioritizing variants in whole-exome sequencing data. Features extensive filtering, clustering, and enrichment capabilities without requiring complex bioinformatics skills.

Python Flask Exome-Seq
Learn More

ONTdeCIPHER

Nanopore-based pipeline for tracking pathogenic variants. Developed for real-time monitoring of SARS-CoV-2 and other pathogen variants using Oxford Nanopore sequencing.

Nanopore Snakemake Variant Calling
Learn More

NGS Analysis Pipelines

Comprehensive suite of bioinformatics pipelines for multi-omics analysis including RNA-Seq, ATAC-Seq, ChIP-Seq, and single-cell sequencing with automated QC and reporting.

Snakemake Nextflow Docker

ML for Genomics

Machine learning models for biomarker identification and predictive analysis in cancer genomics using TensorFlow and scikit-learn frameworks.

TensorFlow scikit-learn Python

Get in Touch

I'm always interested in discussing new opportunities, collaborations, and innovative projects in bioinformatics and data science.

Professional Email

mohammad.salma@igmm.cnrs.fr

Location

Montpellier, France